Nucleic acid-based tests for rhd typing, gender determination and nucleic acid quantification

ABSTRACT

The invention in part provides nucleic acid-based assays, which are particularly useful for non-invasive prenatal testing. The invention in part provides compositions and methods for RhD typing, detecting the presence of fetal nucleic in a sample, determining the relative amount of fetal nucleic acid in a sample and determining the sex of a fetus, wherein each of the assays may be performed alone or in combination.

RELATED APPLICATIONS

This patent application is a continuation of U.S. patent applicationSer. No. 12/027,954 filed on Feb. 7, 2008, entitled NUCLEIC ACID-BASEDTESTS FOR RHD TYPING, GENDER DETERMINATION AND NUCLEIC ACIDQUANTIFICATION, naming Paul Andrew Oeth, Mathias Ehrich, and Min SeobLee as inventors and designated by Attorney Docket No. SEQ-6005-UT,which claims the benefit of U.S. Provisional Patent Application No.60/888,942 filed on Feb. 8, 2007, entitled NUCLEIC ACID-BASED TESTS FORRHD TYPING, GENDER DETERMINATION AND NUCLEIC ACID QUANTIFICATION, namingPaul Andrew Oeth and Mathias Ehrich as inventors and designated byAttorney Docket No. SEQ-6005-PV. The entirety of each of these patentapplications is incorporated herein by reference, including, withoutlimitation, all text, tables and drawings.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII copy, created on May 12, 2008, isnamed SEQ-6005-UT_Seqlist.txt and is 59,263 bytes in size.

FIELD

The invention pertains generally to the field of RhD typing, which findsuse, for example, in prenatal testing.

BACKGROUND

The Rh system is a highly polymorphic blood group system that plays animportant role in haemolytic transfusion reactions, neonatal haemolyticdisease and autoimmune haemolytic anemia. There are two different, buthighly homologous, genes in the Rh system. One gene (RhD) encodes the Dpolypeptide, while the other gene (RHCE) encodes the CcEe polypeptide.RhD carries the D antigen—the most potent blood group immunogen. Thisantigen is absent from a relatively large segment (15-17%) of thepopulation (the Rh-negative phenotype), as a result of RhD gene deletionor other RhD gene alterations (e.g., gene conversion, Pseudogene RhDpsi). As used herein the term “psi” refers to the Greek symbol “ψ.” RHCEexists in four allelic forms and each allele determines the expressionof two antigens in Ce, ce, cE or CE combination (RHCE is the collectivename of the four alleles).

Tests for determining RhD type are critical for a wide range ofapplications. When blood of a rhesus D (RhD) positive donor is given toan RhD negative patient there is a high chance that alloantibodyformation occurs. RhD antibodies will lead to rapid destruction ofRhD-positive red cells and to transfusion reactions. Furthermore, when awoman with red cell or platelet antibodies becomes pregnant, thoseantibodies can cross the placenta and can destruct the red cells or theplatelets of the unborn child.

In the past, nucleic acid-based RhD typing was performed on fetalnucleic acid procured through invasive means. However, conventionalinvasive sampling techniques that analyze fetal DNA from amniotic fluidor chorionic villus are costly and may lead to miscarriage andsensitization of the mother. An alternative source of fetal DNA wasshown to be maternal plasma and serum (Lo et al., Lancet 350, 485-487(1997)).

SUMMARY

Recent years have shown a significant increase in the efforts to usecirculating cell-free fetal DNA in maternal plasma for non-invasiveprenatal diagnostics for example in sex-linked disorders, fetal rhesus Dstatus and beta-thalassaemia (Lo, Y. M. D. et al. Am. J. Hum. Genet. 62,768-775 (1998); and Lo, Y. M. D. et al. N. Engl. J. Med. 339, 1734-1738(1998); both of which are hereby incorporated by reference). In additionto prenatal diagnostics, circulating free fetal nucleic acid may also beused, inter alia, to determine the presence of fetal nucleic acid in asample, to determine the amount of fetal nucleic acid in a sample, andto determine the sex of a fetus. A non-invasive RhD typing test that issensitive and accurate enough to determine the RhD genotype of fetal DNAusing maternal plasma, but also fast, reliable and affordable enough tobe used for a wide range RhD-related applications (e.g., testing donorblood) can serve as an invaluable tool for prenatal diagnostics andblood-related testing.

The invention in part provides nucleic acid-based assays that areparticularly useful for non-invasive prenatal testing. The invention inpart provides compositions and methods for RhD typing, detecting thepresence of fetal nucleic in a sample, determining the relative amountof fetal nucleic acid in a sample, and determining the sex of a fetus,wherein each of the assays may be performed alone or in combination.

The invention in part provides compositions and methods for determiningRhD type. In one embodiment, the compositions and methods of theinvention may be used to determine the presence or absence of one ormore exons in the RhD gene. In a related embodiment, the compositionsand methods of the invention may be used to determine the presence orabsence of any one of exon 4, exon 5, exon 7 or exon 10 in the RhD gene.In a related embodiment, the compositions and methods of the inventionmay be used to determine the presence or absence of the RhD pseudogenepsi. In a related embodiment, the zygosity of the pseudogene psi is alsodetermined. In another related embodiment, the compositions and methodsof the invention may be used to determine the presence or absence ofexon 10 of the RhD gene, whereby the presence of exon 10 acts as apositive control for the occurrence of nucleic acid amplification. Inanother related embodiment, determining RhD type is carried out byannealing an extend primer to a region of the exon, and extending theprimer with one or more nucleotides, chain terminating nucleotides orany combination thereof, further wherein the exon region is selectedsuch that primer extension distinguishes between an RhD exon or RhCexon, and whereby the identity of the primer extension product confirmsthe presence of an RhD exon versus an RhC exon. In some embodiments, theexon region is selected such that primer extension distinguishes betweenan RhD exon or RhD pseudogene exon, and whereby the identity of theprimer extension product confirms the presence of an RhD exon versus anRhD pseudogene exon. In a related embodiment, determining RhD type iscarried out by annealing an extend primer to a region of the exon, andextending the primer with one or more nucleotides, chain terminatingnucleotides or any combination thereof, further wherein the exon regionis selected such that primer extension distinguishes between an RhD geneor RhD psi pseudogene, and whereby the identity of the primer extensionproduct confirms the presence of an RhD gene versus an RhD psipseudogene.

In certain embodiments, a probe oligonucleotide having the nucleotidesequence of an extend primer described herein, or a nucleotide sequencethat is about 90% or more identical (e.g., about 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98% or 99% or more identical) to the sequence of anextend primer, and further wherein the primer still is specific for agiven Rh exon (i.e., specifically hybridizes to a Rh exon) is utilizedin place of an extend primer. In such embodiments, the probeoligonucleotide includes a quenchable, detectable label, such as afluorescent label suitable for use in quantitative polymerase chainreaction detection procedures, for example, known to the person ofordinary skill in the art. Such probe oligonucleotides can be utilizedin detection procedures known to the person of ordinary skill in theart, such as quantitative polymerase chain reaction procedures (utilizedin a quantitative or non-quantitative format). Quantitative polymerasechain reaction procedures often incorporate the use of a polymerasehaving exonuclease activity selected by the person of ordinary skill inthe art.

The invention in part provides compositions and methods to analyze anucleic acid sample for the presence or absence of one or more RhDexons, comprising the steps of amplifying the one or more RhD exons withone or more primer pairs provided in Table 3; determining the presenceor absence of the amplification products from the amplificationreaction, thereby determining the Rh status of an individual. In arelated embodiment, the sample is blood from a pregnant female. In someembodiments, one or more of exon 4, exon 5, exon 7 or exon 10 of the RhDgene. In some embodiments, one or more of exon 4, exon 5, exon 7 or exon10 of the RHCE gene is analyzed. In some embodiments, the exons areanalyzed in a multiplexed amplification reaction. In a relatedembodiment, two or more multiplexed assays are performed in parallel. Insome embodiments, the sample is blood, plasma or serum from a pregnantfemale. In a related embodiment, the sample contains fetal nucleic acidand maternal nucleic acid. In a related embodiment, the RhD status ofthe fetus and mother are determined in a multiplexed amplificationreaction, or a combination of two or more multiplexed reactions. In arelated embodiment, the primer pairs in Table 3 comprise a tag sequenceto improve multiplexing. In some embodiments, the presence or absence ofamplification products is determined by mass spectrometry. In someembodiments, the presence or absence of amplification products isdetermined by detection of hybridization of the amplification productsto a gene chip. In some embodiments, the presence or absence ofamplification products is determined by real time-PCR (alternativelycalled RT-PCR or Q-PCR).

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising amplifying one or more RhD gene exons or fragments thereofwith one or more pairs, or combinations thereof, of amplificationprimers (i) comprising one of the full length nucleotide sequenceshereafter, (ii) comprising one of the underlined nucleotide sequenceshereafter, or (iii) comprising one of the underlined nucleotidesequences hereafter and a tag nucleotide sequence:

Exon 4 (psi zygosity) Primer Pair 1: ACGTTGGATGCTGCCAAAGCCTCTACACG(SEQ ID NO: 1) and ACGTTGGATGTGGCAGACAAACTGGGTGTC; (SEQ ID NO: 2) orExon 4 (psi zygosity) Primer Pair 2: ACGTTGGATGAGAACGGAGGATAAAGATCAGAC(SEQ ID NO: 3) and ACGTTGGATGAGCCAGCATGGCAGACAAACTG, (SEQ ID NO: 4)and analyzing the amplification products from the first step todetermine the presence or absence of one or more RhD gene exons orfragments thereof, wherein the presence or absence of one or more RhDgene exons or fragments thereof is indicative of an Rh genotype. In someembodiments, each primer of the amplification primer pair may comprisethe entire sequence shown or only the underlined sequence, wherein theunderlined portion of the primer is a sequence-specific primer sequenceand the non-underlined portion is a tag sequence for improvedmultiplexing. The tag nucleotide sequence may be any tag sequence knownin the art, or selected by a person of ordinary skill in the art, thatimproves multiplexing (e.g., improves mass spectrometry multiplexing).In some embodiments, the invention in part includes primers that aresubstantially similar to the primers provided herein, for example, aprimer having a nucleotide sequence that is about 90% or more identical(e.g., about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or moreidentical), and further wherein the primer still is specific for a givenRh exon (i.e., specifically hybridizes to a Rh exon). For example, oneor more bases of a primer sequence may be changed or substituted, forexample with an inosine, but the primer still maintains the samespecificity and plexing ability.

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising amplifying one or more RhD gene exons or fragments thereofwith one or more pairs, or combinations thereof, of amplificationprimers (i) comprising one of the full length nucleotide sequenceshereafter, (ii) comprising one of the underlined nucleotide sequenceshereafter, or (iii) comprising one of the underlined nucleotidesequences hereafter and a tag nucleotide sequence:

Exon 4 (psi insertion) Primer Pair 1: ACGTTGGATGGACTATCAGGGCTTGCCCCG(SEQ ID NO: 5) and ACGTTGGATGTGCGAACACGTAGATGTGCA; (SEQ ID NO: 6)and analyzing the amplification products from the first step todetermine the presence or absence of one or more RhD gene exons orfragments thereof, wherein the presence or absence of one or more RhDgene exons or fragments thereof is indicative of an Rh genotype. In someembodiments, each primer of the amplification primer pair may comprisethe entire sequence shown or only the underlined sequence, wherein theunderlined portion of the primer is a sequence-specific primer sequenceand the non-underlined portion is a tag sequence for improvedmultiplexing. The tag sequence may be any tag sequence known in the artthat improves multiplexing (e.g., multiplex analysis by massspectrometry). In some embodiments, the invention in part includesprimers that are substantially similar to the primers provided herein,for example, a primer having a nucleotide sequence that is about 90% ormore identical (e.g., about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99% or more identical), and further wherein the primer still isspecific for a given Rh exon (i.e., specifically hybridizes to a Rhexon).

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising amplifying one or more RhD gene exons or fragments thereofwith one or more pairs, or combinations thereof, of amplificationprimers (i) comprising one of the full length nucleotide sequenceshereafter, (ii) comprising one of the underlined nucleotide sequenceshereafter, or (iii) comprising one of the underlined nucleotidesequences hereafter and a tag nucleotide sequence:

Exon 7 Primer Pair 1: (SEQ ID NO: 7) ACGTTGGATGAATCGAAAGGAAGAATGCCG and(SEQ ID NO: 8) ACGTTGGATGCTGAGATGGCTGTCACCACG;and analyzing the amplification products from the first step todetermine the presence or absence of one or more RhD gene exons orfragments thereof, wherein the presence or absence of one or more RhDgene exons or fragments thereof is indicative of an Rh genotype. In someembodiments, each primer of the amplification primer pair may comprisethe entire sequence shown or only the underlined sequence, wherein theunderlined portion of the primer is a sequence-specific primer sequenceand the non-underlined portion is a tag sequence for improvedmultiplexing. The tag sequence may be any tag sequence known in the artthat improves multiplexing (e.g., multiplex analysis by massspectrometry). In some embodiments, the invention in part includesprimers that are substantially similar to the primers provided herein,for example, a primer having a nucleotide sequence that is about 90% ormore identical (e.g., about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99% or more identical), and further wherein the primer still isspecific for a given Rh exon (i.e., specifically hybridizes to a Rhexon).

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising amplifying one or more RhD gene exons or fragments thereofwith one or more pairs, or combinations thereof, of amplificationprimers (i) comprising one of the full length nucleotide sequenceshereafter, (ii) comprising one of the underlined nucleotide sequenceshereafter, or (iii) comprising one of the underlined nucleotidesequences hereafter and a tag nucleotide sequence:

Exon 7 Primer Pair 1: (SEQ ID NO: 9) ACGTTGGATGAGCTCCATCATGGGCTACAA and(SEQ ID NO: 10) ACGTTGGATGTTGCCGGCTCCGACGGTATC; or Exon 7 Primer Pair 2:(SEQ ID NO: 11) ACGTTGGATGAGCTCCATCATGGGCTACAAC and (SEQ ID NO: 10)ACGTTGGATGTTGCCGGCTCCGACGGTATC,and analyzing the amplification products from the first step todetermine the presence or absence of one or more RhD gene exons orfragments thereof, wherein the presence or absence of one or more RhDgene exons or fragments thereof is indicative of an Rh genotype. In someembodiments, each primer of the amplification primer pair may comprisethe entire sequence shown or only the underlined sequence, wherein theunderlined portion of the primer is a sequence-specific primer sequenceand the non-underlined portion is a tag sequence for improvedmultiplexing. The tag sequence may be any tag sequence known in the artthat improves multiplexing (e.g., multiplex analysis by massspectrometry). In some embodiments, the invention in part includesprimers that are substantially similar to the primers provided herein,for example, a primer having a nucleotide sequence that is about 90% ormore identical (e.g., about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99% or more identical), and further wherein the primer still isspecific for a given Rh exon (i.e., specifically hybridizes to a Rhexon).

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising amplifying one or more RhD gene exons or fragments thereofwith one or more pairs, or combinations thereof, of amplificationprimers (i) comprising one of the full length nucleotide sequenceshereafter, (ii) comprising one of the underlined nucleotide sequenceshereafter, or (iii) comprising one of the underlined nucleotidesequences hereafter and a tag nucleotide sequence:

(SEQ ID NO: 12) ACGTTGGATGACGCTCATGACAGCAAAGTC and (SEQ ID NO: 13)ACGTTGGATGAACTCCATTTTCTCTGACTC; Exon 10 Primer Pair 2: (SEQ ID NO: 14)ACGTTGGATGACTCCATTTTCTCTGACTC and (SEQ ID NO: 12)ACGTTGGATGACGCTCATGACAGCAAAGTC,and analyzing the amplification products from the first step todetermine the presence or absence of one or more RhD gene exons orfragments thereof, wherein the presence or absence of one or more RhDgene exons or fragments thereof is indicative of an Rh genotype. In someembodiments, each primer of the amplification primer pair may comprisethe entire sequence shown or only the underlined sequence, wherein theunderlined portion of the primer is a sequence-specific primer sequenceand the non-underlined portion is a tag sequence for improvedmultiplexing. The tag sequence may be any tag sequence known in the artthat improves multiplexing (e.g., multiplex analysis by massspectrometry). In some embodiments, the invention in part includesprimers that are substantially similar to the primers provided herein,for example, a primer having a nucleotide sequence that is about 90% ormore identical (e.g., about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99% or more identical), and further wherein the primer still isspecific for a given Rh exon (i.e., specifically hybridizes to a Rhexon).

Primer Extension

The invention in part provides compositions and methods to analyze anucleic acid sample for the presence of one or more RhD exons,comprising the steps of amplifying the one or more RhD exons with one ormore primer pairs provided in Table 3; annealing one or more extendprimers to the amplification products of first step, the extend primersprovided in Table 3; performing a primer extension reaction; andanalyzing the primer extension products to determine the Rh status of afetus. The primer extension products may be analyzed using the RhD TestInterpretation Table provided in Table 1. In some embodiments, thepresence or absence of primer extension products is determined by massspectrometry. In some embodiments, the presence or absence of primerextension products is determined by any method known in the art.

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising the steps of amplifying one or more RhD gene exons orfragments thereof with one or more pairs of amplification primers (i)comprising one of the full length nucleotide sequences hereafter, (ii)comprising one of the underlined nucleotide sequences hereafter, or(iii) comprising one of the underlined nucleotide sequences hereafterand a tag nucleotide sequence:

(SEQ ID NO: 1) ACGTTGGATGCTGCCAAAGCCTCTACACG and (SEQ ID NO: 2)ACGTTGGATGTGGCAGACAAACTGGGTGTC; or Exon 4 (psi zygosity) Primer Pair 2:(SEQ ID NO: 3) ACGTTGGATGAGAACGGAGGATAAAGATCAGAC and (SEQ ID NO: 4)ACGTTGGATGAGCCAGCATGGCAGACAAACTG;annealing one or more extend primers to the amplification products fromthe first step, the extend primer comprising:

(SEQ ID NO: 15) gGTCTCCAATGTTCGCGCAGGCAC, or (SEQ ID NO: 16)gGATAAAGATCAGACAGCAAC;extending the primer with one or more nucleotides; and analyzing theprimer extension products to determine the presence or absence of one ormore RhD gene exons or fragments thereof, wherein the presence orabsence of one or more RhD gene exons or fragments thereof is indicativeof an Rh genotype. In some embodiments, each primer of the amplificationprimer pair may comprise the entire sequence shown or only theunderlined sequence, wherein the underlined portion of the primer is asequence-specific primer sequence and the non-underlined portion is atag sequence for improved multiplexing. The tag sequence may be any tagsequence known in the art that improves multiplexing (e.g., multiplexanalysis by mass spectrometry). In some embodiments, the invention inpart includes primers that are substantially similar to theamplification and extend primers provided herein, for example, a primerhaving a nucleotide sequence that is about 90% or more identical (e.g.,about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or moreidentical), and further wherein the primer still is specific for a givenRh exon (i.e., specifically hybridizes to a Rh exon). For example, oneor more bases of a primer sequence may be changed or substituted, forexample with an inosine, but the primer still maintains the samespecificity and plexing ability.

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising the steps of amplifying one or more RhD gene exons orfragments thereof with one or more pairs of amplification primers (i)comprising one of the full length nucleotide sequences hereafter, (ii)comprising one of the underlined nucleotide sequences hereafter, or(iii) comprising one of the underlined nucleotide sequences hereafterand a tag nucleotide sequence:

(SEQ ID NO: 5) ACGTTGGATGGACTATCAGGGCTTGCCCCG and (SEQ ID NO: 6)ACGTTGGATGTGCGAACACGTAGATGTGCA;annealing one or more extend primers to the amplification products fromthe first step, the extend primer comprising:

(SEQ ID NO: 17) GAACGGAGGATAAAGATCAGA, or (SEQ ID NO: 18)cTGCAGACAGACTACCACATGAAC;extending the primer with one or more nucleotides; and analyzing theprimer extension products to determine the presence or absence of one ormore RhD gene exons or fragments thereof, wherein the presence orabsence of one or more RhD gene exons or fragments thereof is indicativeof an Rh genotype. In some embodiments, each primer of the amplificationprimer pair may comprise the entire sequence shown or only theunderlined sequence, wherein the underlined portion of the primer is asequence-specific primer sequence and the non-underlined portion is atag sequence for improved multiplexing. The tag sequence may be any tagsequence known in the art that improves multiplexing (e.g., multiplexanalysis by mass spectrometry). In some embodiments, the invention inpart includes primers that are substantially similar to theamplification and extend primers provided herein, for example, a primerhaving a nucleotide sequence that is about 90% or more identical (e.g.,about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or moreidentical), and further wherein the primer still is specific for a givenRh exon (i.e., specifically hybridizes to a Rh exon).

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising the steps of amplifying one or more RhD gene exons orfragments thereof with one or more pairs of amplification primers (i)comprising one of the full length nucleotide sequences hereafter, (ii)comprising one of the underlined nucleotide sequences hereafter, or(iii) comprising one of the underlined nucleotide sequences hereafterand a tag nucleotide sequence:

(SEQ ID NO: 7) ACGTTGGATGAATCGAAAGGAAGAATGCCG and (SEQ ID NO: 8)ACGTTGGATGCTGAGATGGCTGTCACCACG;annealing one or more extend primers to the amplification products fromthe first step, the extend primer comprising:

(SEQ ID NO: 19) ATGCCGTGTTCAACACCTACTATGCT, (SEQ ID NO: 20)GATGGCTGTCACCACGCTGACTGCTA, or (SEQ ID NO: 21) tTGTCACCACGCTGACTGCTA;extending the primer with one or more nucleotides; and analyzing theprimer extension products to determine the presence or absence of one ormore RhD gene exons or fragments thereof, wherein the presence orabsence of one or more RhD gene exons or fragments thereof is indicativeof an Rh genotype. In some embodiments, each primer of the amplificationprimer pair may comprise the entire sequence shown or only theunderlined sequence, wherein the underlined portion of the primer is asequence-specific primer sequence and the non-underlined portion is atag sequence for improved multiplexing. The tag sequence may be any tagsequence known in the art that improves multiplexing (e.g., multiplexanalysis by mass spectrometry). In some embodiments, the invention inpart includes primers that are substantially similar to theamplification and extend primers provided herein, for example, a primerhaving a nucleotide sequence that is about 90% or more identical (e.g.,about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or moreidentical), and further wherein the primer still is specific for a givenRh exon (i.e., specifically hybridizes to a Rh exon).

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising the steps of amplifying one or more RhD gene exons orfragments thereof with one or more pairs of amplification primers (i)comprising one of the full length nucleotide sequences hereafter, (ii)comprising one of the underlined nucleotide sequences hereafter, or(iii) comprising one of the underlined nucleotide sequences hereafterand a tag nucleotide sequence:

(SEQ ID NO: 9) ACGTTGGATGAGCTCCATCATGGGCTACAA and (SEQ ID NO: 10)ACGTTGGATGTTGCCGGCTCCGACGGTATC; or Exon 7 Primer Pair 2: (SEQ ID NO: 11)ACGTTGGATGAGCTCCATCATGGGCTACAAC and (SEQ ID NO: 12)ACGTTGGATGTTGCCGGCTCCGACGGTATC;annealing one or more extend primers to the amplification products fromthe first step, the extend primer comprising:

(SEQ ID NO: 22) CTTGCTGGGTCTGCTTGGAGAGATCA;extending the primer with one or more nucleotides; and analyzing theprimer extension products to determine the presence or absence of one ormore RhD gene exons or fragments thereof, wherein the presence orabsence of one or more RhD gene exons or fragments thereof is indicativeof an Rh genotype. In some embodiments, each primer of the amplificationprimer pair may comprise the entire sequence shown or only theunderlined sequence, wherein the underlined portion of the primer is asequence-specific primer sequence and the non-underlined portion is atag sequence for improved multiplexing. The tag sequence may be any tagsequence known in the art that improves multiplexing (e.g., multiplexanalysis by mass spectrometry). In some embodiments, the invention inpart includes primers that are substantially similar to theamplification and extend primers provided herein, for example, a primerhaving a nucleotide sequence that is about 90% or more identical (e.g.,about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or moreidentical), and further wherein the primer still is specific for a givenRh exon (i.e., specifically hybridizes to a Rh exon).

In a related embodiment, the invention in part provides a method ofanalyzing a sample comprising nucleic acid to determine an Rh genotype,comprising the steps of amplifying one or more RhD gene exons orfragments thereof with one or more pairs of amplification primers (i)comprising one of the full length nucleotide sequences hereafter, (ii)comprising one of the underlined nucleotide sequences hereafter, or(iii) comprising one of the underlined nucleotide sequences hereafterand a tag nucleotide sequence:

(SEQ ID NO: 12) ACGTTGGATGACGCTCATGACAGCAAAGTC and (SEQ ID NO: 13)ACGTTGGATGAACTCCATTTTCTCTGACTC; Exon 10 Primer Pair 2: (SEQ ID NO: 14)ACGTTGGATGACTCCATTTTCTCTGACTC and (SEQ ID NO: 12)ACGTTGGATGACGCTCATGACAGCAAAGTC;annealing one or more extend primers to the amplification products fromthe first step, the extend primer comprising:

(SEQ ID NO: 15) gGTCTCCAATGTTCGCGCAGGCAC;extending the primer with one or more nucleotides; and analyzing theprimer extension products to determine the presence or absence of one ormore RhD gene exons or fragments thereof, wherein the presence orabsence of one or more RhD gene exons or fragments thereof is indicativeof an Rh genotype. In some embodiments, each primer of the amplificationprimer pair may comprise the entire sequence shown or only theunderlined sequence, wherein the underlined portion of the primer is asequence-specific primer sequence and the non-underlined portion is atag sequence for improved multiplexing. The tag sequence may be any tagsequence known in the art that enables multiplexing. In someembodiments, the invention in part includes primers that aresubstantially similar to the amplification and extend primers providedherein, for example, a primer having a nucleotide sequence that is about90% or more identical (e.g., about 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98% or 99% or more identical), and further wherein the primer stillis specific for a given Rh exon (i.e., specifically hybridizes to a Rhexon).

In another related embodiment, the invention in part provides a methodof analyzing a sample derived from a pregnant female for the presence ofone or more of exon 4, exon 5, exon 7 or exon 10 of the RhD gene fromfetal nucleic acid, and exon 10 of the RhD gene from maternal nucleicacid, comprising the steps of amplifying the RhD nucleic acid with oneor more primer pairs provided in Table 3; determining the presence orabsence of the amplification products from the first step, therebydetermining the Rh status of a fetus. In an optional embodiment, thepresence or absence of exon 10 of the RhD gene may serve as a positivecontrol for the occurrence of nucleic acid amplification or a primerextension reaction. In another related embodiment, a primer extensionreaction is performed to determine the presence or absence of one ormore of exon 4, exon 5, exon 7 or exon 10 of the RhD gene from fetalnucleic acid, and exon 10 of the RhD gene from maternal nucleic acid,wherein the extend primers are provided in Table 3.

The amplification products and/or primer extension products may bedetected by any detection method known in the art, which includes but isnot limited to RT-PCR, mass spectrometry and hybridization to a genechip.

In one embodiment, the primer extension reaction includes theincorporation of a chain terminating nucleotide. In a relatedembodiment, the chain terminating nucleotide is a dideoxynucleotide,dideoxybromouridine or acyclonucleotide. In some embodiments, theextension reaction comprises incorporation of a deoxynucleotide, adideoxynucleotide or a combination thereof. In some embodiments, theextension reaction comprises incorporation of a labeled nucleotide. In arelated embodiment, the extension reaction comprises using a mixture oflabeled and unlabeled nucleotides. In another related embodiment, thelabeled nucleotide is labeled with a molecule selected from the groupconsisting of radioactive molecule, fluorescent molecule, mass label,antibody, antibody fragment, hapten, carbohydrate, biotin, derivative ofbiotin, phosphorescent moiety, luminescent moiety,electrochemiluminescent moiety, chromatic moiety, and moiety having adetectable electron spin resonance, electrical capacitance, dielectricconstant and electrical conductivity. In another related embodiment, thelabeled nucleotide is labeled with a fluorescent molecule.

The invention in part provides compositions and methods to detect thepresence or absence of a target nucleic acid in a sample. In oneembodiment, the compositions and methods of the invention may be used todetect the presence or absence of fetal nucleic acid in a maternalsample. In one embodiment, compositions and methods are provided foranalyzing a plurality of polymorphisms in a nucleic acid sample of fetalorigin; and analyzing a plurality of polymorphisms in a nucleic acidsample of maternal origin, whereby the presence of at least onepolymorphism in the nucleic acid sample of fetal origin, which is notpresent in the nucleic acid sample of maternal origin, confirms thepresence of fetal nucleic acid in the fetal nucleic acid sample. In arelated embodiment, the presence of at least one polymorphism in thenucleic acid sample of fetal origin, which is not present in the nucleicacid sample of maternal origin, is a paternally-inherited allele. Insome embodiments, the same polymorphisms are analyzed in fetal nucleicacid and maternal nucleic acid. In some embodiments, the polymorphism isheterozygous. The plurality of polymorphisms may include 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40,45, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900,1000 or more polymorphisms. In a related embodiment, the polymorphism isa single nucleotide polymorphism (SNP), insertion/deletion, short tandemrepeats (STRs), RFLPs or any other alternate form of a gene, genomic DNAor non-coding region of DNA that occupies the same position on achromosome. The polymorphism may be naturally-occurring or synthetic.Synthetic polymorphisms may include alternative forms introduced on asynthetic oligonucleotide that serve as a competitor or control.

In a related embodiment, the invention in part provides compositions andmethods of determining the presence or absence of fetal nucleic acid inthe sample using the fetal identifiers set forth in Table 3 or 4. In oneembodiment, the method of detecting the presence or absence of fetalnucleic acid in a sample comprises obtaining or possessing a nucleicacid sample known to be of maternal origin and suspected of comprisingfetal nucleic acid; analyzing the nucleic acid sample to determine thematernal genotype of at one or more nucleotide polymorphisms selectedfrom the group consisting of the polymorphisms set forth in Table 3 or4; and analyzing the nucleic acid sample to determine the fetal genotypeof one or more nucleotide polymorphisms selected from the groupconsisting of the polymorphisms set forth in Table 3 or 4, wherein afetal genotype possessing a paternally-inherited allele indicates thepresence of fetal nucleic acid. In a related embodiment, the maternalgenotypes are determined from DNA that is substantially free of fetalnucleic acid. For example, in the case when the sample is blood, thematernal genotypes may be determined from the portion of the blood thatcomprises nucleated maternal cells (e.g., white blood cells). In oneembodiment, the DNA that is substantially free of fetal nucleic acid isfrom peripheral blood mononuclear cells. In some embodiments, the amountof fetal DNA is determined by comparing the relative amount ofpaternally-inherited alleles to maternally-inherited alleles in fetalnucleic acid.

In certain embodiments, the compositions and methods of the inventionmay be used to detect the presence or absence of the Y-chromosome in amaternal sample, which may be used to determine the sex of a fetus. Thepresence or absence of the Y-chromosome in a maternal sample may bedetermined by performing the SRY assay provided herein. The SRY assay isa highly sensitive quantitative internal standard assay that detectstrace amounts of the Y-chromosome.

The presence or absence of the Y-chromosome in a maternal sample mayalso be determined by performing the AMG assay provided herein. Thepresence or absence of a target nucleic acid may be determined incombination with other assays, such as an RhD assay or sex test assay.The methods may also be used for other applications, including but notlimited to, paternity testing, forensics or quality control assays.

The invention in part also provides compositions and methods todetermine the relative amount of target nucleic acid in a sample (e.g.,fetal nucleic acid in a pregnant female sample). In one embodiment, thecompositions and methods of the invention may be used to quantitate therelative amount of the alleles at a heterozygous polymorphic site,wherein said heterozygous polymorphic site has been identified bydetermining the sequence of alleles at a polymorphic site from templateDNA obtained from a maternal sample, wherein said relative amount isexpressed as a ratio, wherein said ratio indicates the relative amountof fetal nucleic acid present in the maternal sample. In a relatedembodiment, the polymorphic sites are provided in Table 3 or 4, 3 or 4.In some embodiments, the polymorphic site is an insertion/deletion, STRor RFLP.

In a related embodiment, the invention in part provides compositions andmethods to determine the relative amount of fetal DNA in a sample (e.g.,plasma of a pregnant woman carrying a male fetus), which comprisesannealing one or more X and Y-specific AMG sequences to the fetal DNA,the primers provided in FIG. 3A-3C; performing a primer extensionreaction; and analyzing the primer extension products to determine theratio of the X and Y-specific extension products. In a relatedembodiment, the fetal AMG amplicon is first amplified using theamplification primers provided in FIGS. 3A-3C. In another relatedembodiment, the competitors provided in FIGS. 3A-3C are introduced as aninternal standard to determine copy number.

In a related embodiment, the invention in part provides compositions andmethods to determine the relative amount of target nucleic acid in asample (e.g., fetal nucleic acid in plasma of a pregnant woman carryinga male fetus). In one embodiment, one or more Y-specific SRY sequencesare annealed to the fetal DNA, the primer comprising GTTACCCGATTGTCCTAC(SEQ ID NO: 23); performing a primer extension reaction; and analyzingthe primer extension products to determine the presence and relativeamount of Y-specific extension products. In a related embodiment, thefetal SRY amplicon is first amplified using the following amplificationprimer pair:

(SEQ ID NO: 24) ACGTTGGATGAGCATCTAGGTAGGTCTTTG and (SEQ ID NO: 25)ACGTTGGATGAGCAACGGGACCGCTACAG.

In some embodiments, the total copy number of nucleic acid molecules forthe human serum albumin (ALB) gene is determined. Methods fordetermining the total copy number of nucleic acid present in a samplecomprise detecting albumin-specific extension products and comparing therelative amount of the extension products to competitors introduced tothe sample. In a related embodiment, the invention in part providescompositions and methods to determine the relative amount of fetal DNAin a sample (e.g., plasma of a pregnant woman carrying a male fetus),which comprises annealing one or more albumin gene sequences to thefetal DNA, the primers provided in FIG. 4; performing a primer extensionreaction; and analyzing the primer extension products to determine therelative amount of ALB extension products. In a related embodiment, thefetal ALB amplicon is first amplified using the amplification primersprovided in FIG. 4. The assay is useful to measure how much nucleic acid(e.g., total copy number) is present in a sample or loaded into aparticular reaction. The assay may serve as an internal control and aguide to the likelihood of success for a particular PCR reaction. Forexample, if only 400 copies of ALB are measured then the probability ofdetecting any fetal DNA may be considered low. In another relatedembodiment, the competitors provided in FIG. 4 are introduced as aninternal standard to determine copy number. In one embodiment, 200, 300,400, 500, 600, 700, 800 or more competitors are introduced to the assay.

The methods of the present invention may be performed alone or incombination with other tests.

In one embodiment the sample is blood. In certain embodiments, thesample is blood from a pregnant female. In a related embodiment, theblood is obtained from a human pregnant female when the fetus is at agestational age selected from the group consisting of: 0-4, 4-8, 8-12,12-16, 16-20, 20-24, 24-28, 28-32, 32-36, 36-40, 40-44, 44-48, 48-52,and more than 52 weeks. In another related embodiment, the sample isobtained through non-invasive means. In some embodiments, the nucleicacid is obtained from plasma from said blood. In some embodiments, thenucleic acid is obtained from serum from said blood. In someembodiments, the sample comprises a mixture of maternal DNA and fetalDNA. While the invention is not limited by how the sample is obtained,the methods and compositions of the invention are particularly usefulfor assaying samples obtained by non-invasive means, which may containlower amounts of nucleic acid to be assayed. In a related embodiment,the sample is processed to selectively enrich fetal nucleic acid. Inanother related embodiment, the maternal and fetal Rh genotypes aredetermined in a multiplexed assay, or a combination of two or moremultiplexed reactions. In a further related embodiment, the maternal Rhgenotype is determined by analyzing maternal nucleic acid from maternalnucleated cells, for example, peripheral mononuclear blood cells (PMBC).

The invention in part utilizes multiplexed reactions to improvethroughput and reduce cost. Thus, provided herein are optimized methodsfor performing a primer mass extension assay, including an optimized PCRamplification reaction that produces amplified targets for subsequentmultiplexed primer mass extension genotyping analysis using massspectrometry. Also provided herein are optimized methods for performingmultiplexed amplification reactions and multiplexed primer massextension reactions in a single well to further increase the throughputand reduce the cost per genotype for primer mass extension reactions.The nucleic acid target-region amplification and primer mass extensiongenotyping reactions have been optimized herein to permit moderate tohigh level multiplexing reactions with greater efficiency and accuracy,while at the same time not adversely affecting the mass spectrometryanalysis of mass extension products.

In one embodiment, the amplification primers provided in Table 3comprises a 5′ tag and a gene-specific sequence (underlined). The tag isused to assist in the amplification of the nucleic acids. The primertags may serve to stabilize the primer during amplification or they mayserve as universal primer sites. More specifically, once the RhD genenucleic acids have been PCR amplified using the primers, primers to thetags are used to further amplify the sequences. In one embodiment, bothamplification steps are performed simultaneously. As will be appreciatedby those skilled in the art, primers without the 5′ tag (primersequences underlined in the Table) can be used in the method of theinvention in order to amplify the RhD gene nucleic acids. Alternatively,the primer sequences can comprise different tag sequences than the tagsindicated in the Table. Tag sequences useful for multiplex amplificationreactions are well known in the art.

In some embodiments, the amplification primers allow for sequencespecific amplification. For example, the PCR primers are designed todiscriminate against amplification of the RHCE gene by taking advantageof sequence differences between the RHD and RHCE gene. In someembodiments, the extend primer of the post-PCR primer extension reactionis designed to target a sequence difference between RHD and RHCE gene sothat any leakage in the allele-specific amplification would lead to adistinguishable primer extension product that does not interfere withcorrect interpretation of RHD detection.

In particular embodiments, a sequence tag is attached to a plurality ofprimary and secondary primer pairs provided in Table 3. The sequence tagcan be attached to either one or both of the primary and secondaryprimers from each pair. Typically, the sequence tag is attached to theprimary and secondary primer of each pair. The sequence tags used hereincan range from 5 up to 20, from 5 up to 30, from 5 up to 40, or from 5up to 50 nucleotides in length, with a sequence tag of 10-mer lengthbeing particularly useful in the methods provided herein. The sequencetag need not be the same sequence for each primer pair in themultiplexed amplification reaction, nor the same sequence for a primaryand secondary primer within a particular amplification pair. In aparticular embodiment, the sequence tag is the same for each primer inthe multiplexed amplification reaction. For example, in certainembodiments, the sequence tag is a 10-mer, such as -ACGTTGGATG- (SEQ IDNO: 26), and is attached to the 5′ end of each primary and secondaryprimer. In particular embodiments of the methods provided herein, only asingle primer pair is used to amplify each particular nucleic acidtarget-region.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1F provide the location design of the RhD primers. Theamplification primers are highlighted and the extend primers are inbold. The Figures also provide the extend primer product associated witheach respective assay result. For example, in FIG. 1A, an extensionproduct with an adenine (A) chain terminating nucleotide indicates thepresence of exon 4 of the RhD gene, an extension product with an adenineand a thymine (A & T) chain terminating nucleotide indicates thepresence of exon 4 of the RhD psi pseudogene, and an extension productwith a cytosine (C) chain terminating nucleotide indicates the presenceof exon 4 of the RHCE gene. FIG. 1A discloses SEQ ID NOS 5-6, 18 and174-176, respectively, in order of appearance. FIG. 1B discloses SEQ IDNOS 3-4, 177 and 174-175, respectively, in order of appearance. FIG. 10discloses SEQ ID NOS 7-8, 19-20 and 178-179, respectively, in order ofappearance. FIG. 1D discloses SEQ ID NOS 180-184, respectively, in orderof appearance. FIG. 1E discloses SEQ ID NOS 11, 10 and 185-187,respectively, in order of appearance. FIG. 1F discloses SEQ ID NOS 12-13and 188-190, respectively, in order of appearance.

FIG. 2 provides the location design of the SRY primers in the SRY genecoding sequence (SEQ ID NO: 191). The amplification primers arehighlighted and the extend primers are underlined. Where the PCR primersare provided alone, the sequence-specific portion of the primer isunderlined, and the multiplex tag is not underlined. In addition,competitor sequences are provided. FIG. 2 discloses SEQ ID NOS 192-201,25, 24, 202-212, respectively, in order of appearance.

FIG. 3A-3C provide the location design of the AMG primers. Theamplification primers are underlined once and the extend primers areunderlined twice. In addition, competitor sequences are provided. FIG.3C includes a Results Table that shows the different masses generated byeach of the AMG and SRY assays, which may be used to interpret theresults from the assays. FIG. 3A discloses SEQ ID NOS 213-221,respectively, in order of appearance. FIG. 3B discloses SEQ ID NOS213-214 and 222-226, respectively, in order of appearance. FIG. 3Cdiscloses SEQ ID NOS 213-241, 227-228, 217, 229-231, 217, 230, 232-233,194 and 234, respectively, in order of appearance.

FIG. 4 provides the location design of the albumin (ALB) primers. Theamplification primers are highlighted and the extend primer isunderlined twice. Where the PCR primers are provided alone, thesequence-specific portion of the primer is underlined, and the multiplextag is not underlined. In addition, competitor sequences are provided.FIG. 4 discloses SEQ ID NOS 235-241, respectively, in order ofappearance.

FIG. 5 shows the use of single nucleotide polymorphisms (SNP's) FetalIdentifiers to confirm the presence of fetal DNA by paternally-inheritedalleles.

FIG. 6 shows representative mass spectra demonstrating the correlationbetween fetal DNA amounts estimated from AMG XY and from FetalIdentifier assays. The results were generated using the AMG primersprovided in FIG. 3.

FIG. 5 depicts the validation scheme, performance criteria and modelsystem used to qualify multiplex SNP assays for their utility inidentifying the presence for fetal DNA.

FIG. 8 depicts typical performance results for a qualified fetalidentifier. Here the ability of the SNP assay to estimate the quantityof fetal DNA in the background of maternal DNA was verified for a totalof 1700 copies and a total of 170 copies using genomic DNA mixtures.Note that the standard deviation of the estimate of fetal DNA increasesdue to the significant influence of the sampling error at low copynumbers

FIG. 9 shows the performance of multiplexed SNP assays (21 assays total)for detection of paternally-inherited alleles in a model system.

FIG. 10 (provided in duplicate) shows different multiplexed assayschemes of the invention.

DETAILED DESCRIPTION

The determination of fetal Rh genotypes from maternal plasma is usuallyperformed by PCR amplification of individual RhD exons. Negative testresults, in particular for female fetuses, can require additional testsconfirming the presence of sufficient amounts of fetal DNA. Thecompositions and methods of the invention offer nucleic acid-based testsfor determining Rh type and determining the relative amount of targetnucleic acid in a sample. The tests are particularly useful for prenataldiagnostics, wherein the presence and relative amount of fetal nucleicacid in a maternal sample can be determined, and further wherein fetaland maternal Rh type can be determined in a highly sensitive, accuratemultiplexed reaction. The invention, therefore, provides an alternativemethod that further comprises high-frequency single nucleotidepolymorphisms (SNPs) to determine the amount of fetal nucleic acidpresent in a sample, which in turn reduces the number of inconclusivetests.

The test primers were designed to ensure that the exon sequence forexons 4, 5, 7 and 10 inclusive of RhD is amplified by the RhD MPX PCR ofthe invention. The location design of the RhD primers is illustrated inFIGS. 1A-1F.

The assays provided herein offer many advantageous over existing RhDtyping methods. Specifically, the multiplexed test reagents address thelimited availability of fetal nucleic acid, complexity of geneticchanges and high quality testing. The multiplexed RhD/Fetal Identifierassays allow for comprehensive non-invasive Rh genotyping of fetal DNAin only two reactions, while guarding against false-interpretation ofnegative test results caused by insufficient amounts of fetal DNA.Alternatively, the reactions are performed in a single, multiplexedreaction. The assays have built in quality controls to improve theaccuracy of results. The RhDψ pseudogene is recognized even inheterozygote state. The SRY assay is highly sensitive and specific forpaternal alleles, and the determination of maternal baseline requiresonly one additional reaction. Finally, the assay can be used foranalysis of adult blood donor subjects. This is important in connectionwith subjects who receive frequent transfusions, for example, those withsickle cell anemia.

In one embodiment, the invention also relates to a method fordetermining whether a patient in need of a blood transfusion is to betransfused with RhD negative blood from a donor. The invention hasimportant implications for devising a transfusion therapy in humans. Forexample, it can now be conveniently tested whether the patient actuallyneeds a transfusion with a RhD negative blood or whether suchprecautions need not be taken.

As used herein, “sample” refers to a composition containing a materialto be detected or analyzed. Samples include “biological samples”, whichrefer to any material obtained from a living source, for example, ananimal such as a human or other mammal, a plant, a bacterium, a fungus,a protist or a virus or a processed form, such as amplified or isolatedmaterial. The sample may be obtained through invasive (e.g.,amniocentesis) or non-invasive (e.g., blood draw) means. In a preferredembodiment, the sample is obtained non-invasively. The biological samplecan be in any form, including a solid material such as a tissue, cells,a cell pellet, a cell extract, a biopsy, or feces, or a biological fluidsuch as urine, whole blood, plasma, serum, interstitial fluid, vaginalswab, pap smear, peritoneal fluid, lymph fluid, ascites, sweat, saliva,follicular fluid, breast milk, non-milk breast secretions, cerebralspinal fluid, seminal fluid, lung sputum, amniotic fluid, exudate from aregion of infection or inflammation, a mouth wash containing buccalcells, synovial fluid, or any other fluid sample produced by thesubject. In addition, the sample can be solid samples of tissues ororgans, such as collected tissues, including bone marrow, epithelium,stomach, prostate, kidney, bladder, breast, colon, lung, pancreas,endometrium, neuron, muscle, and other tissues. Samples can includeorgans, and pathological samples such as a formalin-fixed sampleembedded in paraffin. If desired, solid materials can be mixed with afluid or purified or amplified or otherwise treated. Samples examinedusing the methods described herein can be treated in one or morepurification steps in order to increase the purity of the desired cellsor nucleic acid in the sample. Samples also can be examined using themethods described herein without any purification steps to increase thepurity or relative concentration of desired cells or nucleic acid. Asused herein, the term “blood” encompasses whole blood or any fractionsof blood, such as serum and plasma as conventionally defined.

The terms “nucleic acid” and “nucleic acid molecule” may be usedinterchangeably throughout the disclosure. The terms refer to adeoxyribonucleotide (DNA), ribonucleotide polymer (RNA), RNA/DNA hybridsand polyamide nucleic acids (PNAs) in either single- or double-strandedform, and unless otherwise limited, would encompass known analogs ofnatural nucleotides that can function in a similar manner as naturallyoccurring nucleotides.

As used herein, the term “amplifying” or “amplification” refers to meansfor increasing the amount of a biopolymer, especially nucleic acids.Based on the 5′ and 3′ primers that are chosen, amplification alsoserves to restrict and define a target-region or locus of the genomewhich is subject to analysis. Amplification can be by any means known tothose skilled in the art, and in particular embodiments, includes theuse of the polymerase chain reaction (PCR). The phrase simultaneousamplification refers to the amplification of 2 or more nucleic acidtarget-regions at the same time. The simultaneous amplification istypically within the same amplification mixture.

As used herein, the term “multiplexing” refers to the simultaneousamplification or primer mass extension reaction of more than oneoligonucleotide or primer (e.g., in a single reaction container); or thesimultaneous analysis of more than one oligonucleotide, in a single massspectrometric or other mass measurement, i.e., a single mass spectrum orother method of reading sequence.

As used herein, the phrase “simultaneous amplification” refers to themultiplexed amplification of 2 or more loci or nucleic acidtarget-regions in a single reaction mixture. Simultaneous amplificationtherefore encompasses 5 or more, 6 or more, 7 or more, 8 or more, 9 ormore, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 ormore, 16 or more, 17 or more, 18 or more, 19 or more, 20 or more, 30 ormore, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 100 ormore, 200 or more, 500 or more, 1000 or more, 2000 or more amplificationreactions. The amplification of each particular target-region occurs inparallel at the same time. Although it is contemplated herein that thesimultaneous amplifications can occur in separate reaction mixtures, forthe methods provided herein the simultaneous amplification reactionstypically occur in the same single reaction. Likewise multiplexed primermass extension refers to the simultaneous extension of 2 or moregenotyping primers in a single reaction mixture. Accordingly,multiplexed primer mass extension therefore encompasses [5 or more, 6 ormore, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 ormore, 13 or more, 14 or more, 15 or more, 16 or more, 17 or more, 18 ormore, 19 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 ormore, 70 or more, 80 or more, 100 or more, 200 or more, 500 or more,1000 or more, 2000 or more primer mass extension reactions. Multiplexedamplification and primer mass extension reactions also encompass 21, 22,23, 24, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80, 100,1000 or more reactions.

As used herein, the phrase “target nucleic acid” refers to one or morenucleic acids, such as genomic DNA, from which one or more regions orloci are to be amplified.

As used herein, the phrase “nucleic acid-target region” refers to theregion-specific areas or loci of a target nucleic acid (e.g., UTR, exonor intron) that are amplified for subsequent sequence variationanalysis. The amplified nucleic acid-target regions each contain atleast one sequence variation or site that is being genotyped.

As used herein, the term “polymorphism” refers to the coexistence ofmore than one form or allele of a nucleic acid, such as a chromosome, orportion thereof. For example, a portion or locus of a gene at whichthere are at least two different alleles, i.e., two different nucleotidesequences, is referred to as a polymorphic loci, site or region of agene. A polymorphic loci can be a single nucleotide (e.g., SNP) or canbe several nucleotides in length (e.g., insertions or deletions).Accordingly, polymorphism includes substitutions, insertions,duplications and deletions of nucleotides. A polymorphism can also referto a particular nucleotide(s) or nucleotide sequence occurring at aparticular polymorphic site.

As used herein, the term “genotyping” refers to the process ofdetermining the particular nucleotide or nucleotides (e.g., sequencevariation) either present or absent at a particular polymorphic loci orgenomic location.

As used herein, “allele”, which is used interchangeably herein with“allelic variant” refers to alternative forms of a nucleic acid such asa gene or polymorphic regions thereof. Alleles occupy the same locus orposition (referred to herein as a polymorphic region) on homologouschromosomes. When a subject has two identical alleles of a polymorphicregion within a gene, the subject is said to be homozygous for theallele. When a subject has two different alleles of a polymorphic regionwithin a gene, the subject is said to be heterozygous for the allele.Alleles of a specific gene can differ from each other at a polymorphicregion corresponding to a single nucleotide, or several nucleotides, andcan include substitutions, deletions, insertions and duplications ofnucleotides. An allele of a gene can also be a form of a gene containinga mutation.

As used herein, the term “non-homologous variant” refers to one or moresequence variations that exist between two or more highly homologousgenes (e.g., RhD and RHCE), pseudogenes, transcript variants, repeats orother similar genomic sequences. Non-homologous variants between genescan differ from each other by a single nucleotide, or severalnucleotides, and can include substitutions, deletions, insertions andduplications of nucleotides. For example, an RhD pseudogene exists thatcontains a 37 base pair insertion in exon 4. In the context of thepresent invention, the 37 base pair insertion of the pseudogene isconsidered a non-homologous variant. Non-homologous variants usuallyoccupy the same locus or position on highly homologous genes (e.g., inthe same, corresponding exon or intron). For example, sequencevariations between the highly homologous RhD and RHCE genes areparticularly useful for RhD testing.

As used herein, the term “genotype” refers to the identity of thealleles or non-homologous variants present in an individual or sample.The term “genotyping a sample” or “genotyping an individual” refers todetermining a specific allele or specific nucleotide(s) in a sample orcarried by an individual at particular region(s).

As used herein, the phrase “RhD testing” refers to a DNA-basedgenotyping method to detect the RhD and/or RHCE genes and theirprevalent alleles, non-homologous variants and combinations thereof(e.g., RhD sequence that contains replacements with homologous RHCEsequences). RhD testing may be used to determine an RhD phenotype.

As used herein, the term “Rh phenotype” refers to determining thepresence or absence of antigens of the Rh blood group, specifically redcell antigens C, D and E. An individual is either Rh-positive orRh-negative for a given antigen. For example, “an RhD-negative”individual does not express antigen D, whereas an RhD-positiveindividual does express antigen D. “Rh incompatibility” occurs when redcells from a Rhesus positive fetus cross the placenta and sensitize aRhesus negative mother, especially at parturition. The mother's antibodymay then, in a subsequent pregnancy, cause haemolytic disease of thenewborn if the fetus is Rhesus positive.

Whether detecting sequence differences, detecting amplification productsor primer extension products, any detection method known in the art maybe utilized. While many detection methods include a process in which aDNA region carrying the polymorphic site of interest is amplified, ultrasensitive detection methods which do not require amplification may beutilized in the detection method, thereby eliminating the amplificationprocess. Polymorphism detection methods known in the art include, forexample, primer extension or microsequencing methods, ligase sequencedetermination methods (e.g., U.S. Pat. Nos. 5,679,524 and 5,952,174, andWO 01/27326), mismatch sequence determination methods (e.g., U.S. Pat.Nos. 5,851,770; 5,958,692; 6,110,684; and 6,183,958), microarraysequence determination methods, restriction fragment length polymorphism(RFLP) procedures, PCR-based assays (e.g., TAQMAN® PCR System (AppliedBiosystems)), nucleotide sequencing methods, hybridization methods,conventional dot blot analyses, single strand conformationalpolymorphism analysis (SSCP, e.g., U.S. Pat. Nos. 5,891,625 and6,013,499; Orita et al., Proc. Natl. Acad. Sci. U.S.A 86: 27776-2770(1989)), denaturing gradient gel electrophoresis (DGGE), heteroduplexanalysis, mismatch cleavage detection, and techniques described inSheffield et al., Proc. Natl. Acad. Sci. USA 49: 699-706 (1991), Whiteet al., Genomics 12: 301-306 (1992), Grompe et al., Proc. Natl. Acad.Sci. USA 86: 5855-5892 (1989), and Grompe, Nature Genetics 5: 111-117(1993), detection by mass spectrometry (e.g., US 20050079521, which ishereby incorporated by reference), real time-PCR (e.g., U.S. Pat. No.5,210,015, U.S. Pat. No. 5,487,972, both of which are herebyincorporated by reference), or hybridization with a suitable nucleicacid primer specific for the sequence to be detected. Suitable nucleicacid primers can be provided in a format such as a gene chip.

Primer extension polymorphism detection methods, also referred to hereinas “microsequencing” methods, typically are carried out by hybridizing acomplementary oligonucleotide to a nucleic acid carrying the polymorphicsite. In these methods, the oligonucleotide typically hybridizesadjacent to the polymorphic site. As used herein, the term “adjacent”refers to the 3′ end of the extension oligonucleotide being sometimes 1nucleotide from the 5′ end of the polymorphic site, often 2 or 3, and attimes 4, 5, 6, 7, 8, 9, or 10 nucleotides from the 5′ end of thepolymorphic site, in the nucleic acid when the extension oligonucleotideis hybridized to the nucleic acid. The extension oligonucleotide then isextended by one or more nucleotides, often 1, 2, or 3 nucleotides, andthe number and/or type of nucleotides that are added to the extensionoligonucleotide determine which polymorphic variant or variants arepresent. Oligonucleotide extension methods are disclosed, for example,in U.S. Pat. Nos. 4,656,127; 4,851,331; 5,679,524; 5,834,189; 5,876,934;5,908,755; 5,912,118; 5,976,802; 5,981,186; 6,004,744; 6,013,431;6,017,702; 6,046,005; 6,087,095; 6,210,891; and WO 01/20039. Theextension products can be detected in any manner, such as byfluorescence methods (see, e.g., Chen & Kwok, Nucleic Acids Research 25:347-353 (1997) and Chen et al., Proc. Natl. Acad. Sci. USA 94/20:10756-10761 (1997)) and by mass spectrometric methods (e.g., MALDI-TOFmass spectrometry or electrospray mass spectrometry). Oligonucleotideextension methods using mass spectrometry are described, for example, inU.S. Pat. Nos. 5,547,835; 5,605,798; 5,691,141; 5,849,542; 5,869,242;5,928,906; 6,043,031; 6,194,144; and 6,258,538.

Microsequencing detection methods often incorporate an amplificationprocess that proceeds the extension step. The amplification processtypically amplifies a region from a nucleic acid sample that comprisesthe polymorphic site. Amplification can be carried out by utilizing apair of oligonucleotide primers in a polymerase chain reaction (PCR), inwhich one oligonucleotide primer typically is complementary to a region3′ of the polymorphism and the other typically is complementary to aregion 5′ of the polymorphism. A PCR primer pair may be used in methodsdisclosed in U.S. Pat. Nos. 4,683,195; 4,683,202, 4,965,188; 5,656,493;5,998,143; 6,140,054; WO 01/27327; and WO 01/27329 for example. PCRprimer pairs may also be used in any commercially available machinesthat perform PCR, such as any of the GENEAMP® Systems available fromApplied Biosystems.

A microarray can be utilized for determining whether a polymorphicvariant is present or absent in a nucleic acid sample. A microarray mayinclude any oligonucleotides described herein, and methods for makingand using oligonucleotide microarrays suitable for prognostic use aredisclosed in U.S. Pat. Nos. 5,492,806; 5,525,464; 5,589,330; 5,695,940;5,849,483; 6,018,041; 6,045,996; 6,136,541; 6,142,681; 6,156,501;6,197,506; 6,223,127; 6,225,625; 6,229,911; 6,239,273; WO 00/52625; WO01/25485; and WO 01/29259. The microarray typically comprises a solidsupport and the oligonucleotides may be linked to this solid support bycovalent bonds or by non-covalent interactions. The oligonucleotides mayalso be linked to the solid support directly or by a spacer molecule. Amicroarray may comprise one or more oligonucleotides complementary to apolymorphic site within a nucleotide sequence in Tables 6, 7 or 8.

Fetal Identifiers

Cell-free fetal DNA constitutes only a minor fraction of the total DNAfound in maternal plasma. The amount of fetal DNA in maternal plasma isdependent on the gestational age and is estimated at 3-6%.

Because the analysis is relying on the detection of apaternally-inherited disease-causing sequence, it is vital to be able toascertain that the absence of the disease-causing sequence is a truediagnostic result and not caused by insufficient amount of circulatingfetal DNA or even loss of the fetal DNA during sample processing.

The use of polymorphisms provide a means to confirm the presence offetal DNA and therefore complete the analysis of negative, and otherwiseinconclusive, test result in non-invasive prenatal diagnostics. The useof single nucleotide polymorphisms (SNPs), the most abundant type ofpolymorphism in the human genome, or insertion/deletion (Ins/Del)polymorphisms may serve as fetal identifiers to determine the presenceof fetal DNA in a processed sample (Li, Y., Wenzel, F., Holzgreve, W.,Hahn, S., Genotyping fetal paternally inherited SNPs by MALDI-TOF MSusing cell-free fetal DNA in maternal plasma: Influence of sizefractionation. Electrophoresis 27, 3889-3896 (2006); Van der Schoot, C.E., Rijnders, R. J., Bossers, B., de Haas, M., Christiaens, G. C., Dee,R. Real-time PCR of bi-allelic insertion/deletion polymorphisms canserve as a reliable positive control for cell-free fetal DNA innon-invasive prenatal genotyping [abstract] Blood 102, 93a (2003); andChow, K. C., Chiu, R. W., Tsui, N. B., Ding, C., Lau, T. K., Leung, T.N., Lo, Y. M., Mass Spectrometric detection of a SNP panel as aninternal positive control for fetal DNA analysis in maternal plasma.Clin. Chem. 53, 141-142 (2007), all of which are hereby incorporated byreference).

A SNP is considered informative for the determination of the presence offetal DNA, if the mother is homozygous and the fetus inherited theopposite allele from the father, rendering the genotype of the fetusheterozygous.

To ensure a high probability that the presence of fetal DNA can beconfirmed by the presence of the paternally-inherited allele in at least1 SNP, a sufficient number of SNPs or Ins/Dels with a high populationfrequency (>0.4 for the minor frequent allele) has to be analyzed. Ascheme exemplifying the concept of using SNPs to confirm the presence offetal DNA in maternal plasma is depicted in FIG. 5.

Analysis of multiple polymorphisms in DNA extracted from maternal plasmacreates a two-fold challenge: firstly, the paternally-inherited alleleneeds to be detected in the background of the maternal DNA; secondly,the high number of polymorphisms require significant sample material anda significant number of reactions before a conclusive test result isachieved.

Thus the invention in part provides a multiplexed panel of SNPs toestablish a universal assay panel for non-invasive prenatal diagnostics.

Kits

Furthermore, the invention relates to a kit comprising the compositionsof the invention. Parts of the kit can be packaged individually in vialsor in combination in containers or multicontainer units. The kit of thepresent invention may be advantageously used for carrying out the methodof the invention and could be, inter alia, employed in a variety ofapplications referred to above. The manufacture of the kits followspreferably standard procedures which are known to people skilled in theart.

EXAMPLES

The following examples illustrate but do not limit the invention.

Example 1 RhD Test Analysis of RhD exons and SNPs was enabled bymultiplex PCR followed by multiplexed allele-specific primer extensionand analysis by MALDI-TOF MS. Initial evaluation of the assays wasperformed using genomic DNA. Multiplexes were also evaluated fromartificial mixtures to establish sensitivity and precision of thesemi-quantitative readout of SNP alleles. Final performance wasestablished using cell-free fetal DNA from maternal plasma.

Extraction of cell-free fetal DNA was performed using a modified QiagenMinElute protocol.

Two multiplex reactions were developed that cumulatively integrated thedetection of RhD exons 4, 5, 7, 10 and the detection of the RhD psipseudogene conversion with 16 high-frequent SNPs. The use of 16 SNPsstatistically provides up to 4 assays, which can confirm the presence offetal DNA through detection of the paternally-inherited fetal allele.Performance of the multiplexed assays in artificial mixtures and incell-free fetal DNA extracted from maternal plasma was demonstrated.

The method comprises the following 8 steps:

1. Isolate plasma and peripheral blood mononuclear cells (PBMC) fromwhole blood.2. Purify cell-free DNA from the plasma (designated fetal DNA).3. Purify DNA from PBMC (designated maternal DNA).4. Prepare fetal and maternal DNA working dilutions (0.15 ng/μl).5. Amplify the fetal and maternal DNA.6. Process the Iplex™ Gold extend reactions on the amplified fetal andmaternal DNA.7. Dispense the MassExtend reaction products to a SpectroCH IP® array.8. Analyze samples on the MassARRAY Analyzer Compact.9. Interpret the results using with the aid of Table 1.

TABLE 1 RhD Test Interpretation Test RhD/ RhD/ RhD RhD Inter- RhD psiRhD psi RhD Exon Exon pre- Exon 4 Exon 4 Exon 5 7 10 tation Genedeletion C G C C — RhD− Gene conversion C G C C T RhD− RhD-CE-D; exons 1and 10 of RhD gene present Gene conversion C G C C T RhD− RhD-CE-D;exons 1-3 and 9-10 of RhD gene present Pseudogene RhDy AT A G T T RhD−homozygous Pseudogene RhDy AT AG G T T RhD+ heterzygous Apparentlyintact A G G T T RhD+ RhD gene; possibly bearing single point mutationsRhCE alleles denoted in bold and underlined represent leakage fromallele-specific priming.Any negative result is a true negative.Any positive result is a true positive.Inconclusive results will result in further testing and/or therapy.

Step 5 and 6 are further described herein. Following genomicamplification, the assay interrogates amplified regions through the useof specific primers that are designed to hybridize directly adjacent tothe site of interest. These DNA oligonucleotides are referred to asiPLEX MassEXTEND primers. In the extension reaction, the iPLEX primersare hybridized to the complementary DNA templates and extended with aDNA polymerase. Special termination mixtures that contain differentcombinations of deoxy- and dideoxynucleotide triphosphates along withenzyme and buffer, direct limited extension of the iPLEX primers. Primerextension occurs until a complementary dideoxynucleotide isincorporated.

The extension reaction generates primer products of varying length, eachwith a unique molecular weight. As a result, the primer extensionproducts can be simultaneously separated and detected using MatrixAssisted Laser Desorption/Ionization, Time-Of-Flight(MALDI-TOF) massspectrometry on the MassARRAY® Analyzer Compact. Following thisseparation and detection, SEQUENOM's proprietary software automaticallyanalyzes the data and presents the assay results in the BioReporter RhDreport.

A more specific protocol is provided in the Tables below. Theseconditions are not intended to limit the scope of the invention.

TABLE A PCR Master Mix Preparation (MMX) Final Conc. Volume Volume per50 μl per each per 100 MMX Reagent rxn 50 μl (ul) rxn (ul) MMX1 WaterN/A 7.55 755 10×PCR Buffer (contains 1.25x 6.25 625 15 mM MgCl2,Tris-Cl, KCl, (NH4)2SO4, pH 8.7 (Qiagen) 25 mM MgCl₂ 1.625 mM 3.25 325(Qiagen) PCR Nucleotide Mix 800 μM 1 100 (10 mM each dATP, dCTP, (200 uMdGTP, dUTP) (Roche) each) 2 U/μl Uracil-DNA- 2.5 U/rxn 1.25 125Glycosylase (UDG)(NEB) 5 U/μl HotStar Taq 3.5 U/rxn 0.7 70 (Qiagen) SubTotal for MMX1 20 2000 MMX2 0.5-1.5 uM RhD primers 0.1-0.5 uM 10 1000Mix (Operon/IDT) each MMX Total for MMX 30 3000 Sample DNA ng/ul 20 PCRReaction Total 50

1.2.1 Combine 20 ul of MMX1 and 10 ul of MMX2 to make 30 ul of each PCRMMX.

1.2.2 Add 20 ul of sample (plasma DNA) to MMX

1.2.3 Mix well, seal plate, spin briefly and cycle according tofollowing parameters in table 3.

TABLE B PCR 30-11Cycling Conditions (two steps cycling) Temp. TimeCycles Notes 30 C. 10 min  1 UDG Incubation 94 C. 15 min  1 InitialDenaturation 94 C. 20 sec Target Amplification 56 C. 30 sec {closeoversize brace} 30 cycles 72 C.  1 min 94 C. 20 sec ProductAmplification 62 C. 30 sec {close oversize brace} 11 cycles 72 C.  1 min72 C.  3 min  1 Final Extension  4 C. Forever  1 Hold

1.2.4 10 uL PCR Aliquots

Prepare two iPLEX EXTEND reaction plates by plating 10 uL PCR samplesfrom each well of the PCR plate into two new 96-well plates designatedfor SAP and EXTEND reactions using the liquid handler

1.3 SAP Reaction

1.3.1 Prepare the SAP mixes according to Table 4 below. Dispense 6 μASAP mix to the corresponding wells of one V-bottom Sarstedt 96-wellplate. Transfer 4 μl SAP from the 96-well stock plate to each of the96-well PCR plates, using a Liquid Handler.

TABLE C SAP Cocktail preparation Volume [uL] (60% overhang) ReagentFinal C n = 1 160 Lot# Nanopure Water, n/a 2.95 472 Autoclaved SAPBuffer, 10× 0.85x 0.34 54.4 SAP (1.7 U/ul = 1.2 U/rxn 0.71 113.6transparent label) Total volume [uL] n/a 4 640 n/a

1.3.2 When preparation is finished, seal the plate, vortex, centrifugebriefly and cycle each plate according to the following parameters inthe table below.

TABLE D SAP Thermal Cycling Conditions Temperature Incubation Time PlateID 37° C. 40 minutes Program ID: SAP-40-5 80° C.  5 minutes  4° C. store1.4 iPLEX Extension

TABLE E iPLEX EXTEND Cocktail Mix Preparation Volume [uL] Volume = 1 −(60% Extend Reagent Rxn overhang) 160 Water (HPLC grade) 1.238 198.08iPLEX detergent free 0.4 64 buffer (10×) iPLEX Termination 0.4 64 MixExtend Primer Mix 1.88 300.8 Thermosequenase 0.082 13.12 (32 U/uL) TotalVolume 4 640

-   -   1.4.1 Add 6 ul cocktail to each well of one V-bottom Sarstedt 96        plate. Transfer 4 μl iPLEX-EXTEND cocktail from the V-bottom        Sarstedt 96 plate to each well of the 96-SAP/PCR plates, using a        Matrix MassARRAY Liquid Handler into well positions according to        plate lay out.    -   1.4.2 Seal the plates, vortex, centrifuge briefly and cycle        according to the parameters listed below in Table 10.

TABLE F hME-100 Incubation Temperature Time Cycles Notes 94° C. 2minutes 1 Plate ID: 1) 06-28-2006_HLBK_ST_DOL 94° C. 5 seconds 99 cyclesProgram ID: hME-100 52° C. 5 seconds Cycler ID: BLK0116, BSE 0046 72° C.5 seconds Cycler Bonnet ID (iM applicable):  4° C. forever 1

Example 2 Fetal Identifiers, Sex Test and Copy Number DeterminationSelection of SNPs

Analysis of paternally-inherited alleles in clinical samples andcorrelation with Y-chromosome frequency in male fetuses was performedwith a total of 16 SNPs; SNP assays for analysis of clinical sampleswere multiplexed as 8-plexes; all SNPs had a minor allele frequency(maf) of ˜0.4 in all ethnic groups and were unlinked.

For performance evaluation of a universal Fetal Identifier panel thatcan be multiplexed with disease-specific markers, a new panel of 87 NTSNPs with a pan-ethnic maf >0.4 was selected and multiplexed into16-plexes.

Method of SNP Analysis

Analysis of SNPs in maternal buffy coat and maternal plasma wasperformed using the iPLEX™ assay and MassARRAY® technology (Jurinke, C.,Oeth, P., van den Boom, D., MALDI-TOF mass spectrometry: a versatiletool for high-performance DNA analysis. Mol. Biotechnol. 26, 147-164(2004); and Oeth, P. et al., iPLEX™ Assay: Increased Plexing Efficiencyand Flexibility for MassARRAY® System through single base primerextension with mass-modified Terminators. SEQUENOM Application Note(2005), both of which are hereby incorporated by reference). In brief,the target region surrounding the SNP is first amplified by PCR.Subsequently an oligonucleotide primer is annealed to the PCR productand is extended allele-specifically by a single nucleotide using amixture of 4 terminator nucleotides and a DNA polymerase. The extensionproducts are transferred to a miniaturized chip array and are analyzedby MALDI-TOF Mass Spectrometry. Determination of the molecular mass ofextension products allows unambiguous identification of the SNP allelepresent in the sample. The peak area ratio of mass signals allows theestimation of the relative abundance of the alleles in a given sample.FIG. 6 provides an overview of the assay used for SNP analysis.

Clinical Samples

The total sample set consisted of 35 paired blood/plasma samples frompregnant Caucasian woman (nine 1st trimester; twelve 2nd trimester;fourteen 3rd trimester).

The subset of samples used for correlation of Y-chromosome frequency andpaternally-inherited alleles in maternal plasma consisted of 19 samplesof pregnant Caucasian woman carrying a male fetus.

DNA Extraction

DNA extraction was performed from 1 ml of maternal plasma using theQiagen MinElute kit for fetal genotyping.

DNA extraction from frozen blood (minus plasma) was performed from 4 mlusing Qiagen's PureGene kit for maternal genotyping.

Results

An assay targeting sequence differences in the Amelogenin region on theX and Y chromosome was used to assess the relative amount of fetal DNAextracted from plasma of pregnant woman carrying a male fetus. Detailsof the AMG assay are depicted in FIGS. 3A-3C. X and Y-specific sequencescan be discriminated by sequence specific iPLEX extension products andtheir respective mass signals. The peak area ratio of the extensionproducts allows estimation of the relative amount of fetal DNA, becausethe Y-specific sequences represent 50% of the total fetal DNAcontribution.

Sixteen of nineteen (84%) plasma samples with a male fetus showed aY-chromosome frequency of higher than 5%, indicating presence of atleast 10% fetal DNA in the extracted DNA.

FIG. 8 depicts typical performance results for a qualified fetalidentifier. Here the ability of the SNP assay to estimate the quantityof fetal DNA in the background of maternal DNA was verified for a totalof 1700 copies and a total of 170 copies using genomic DNA mixtures.Note that the standard deviation of the estimate of fetal DNA increasesdue to the significant influence of the sampling error at low copynumbers

Table 2 provides a list of SNPs that were multiplexed at 10+ plexinglevel and passed all phases of the validation shown in FIG. 7.Application of this assay panel to a model system for the detection offetal DNA in maternal background showed that paternally-inherited fetalalleles can be detected with a sensitivity of 95% at 100% specificity ifthe sample preparation method can enrich the relative amount of fetalDNA to 20%. In Table 2, the minor allele frequency (MAF) for each SNPfrom different ethnic populations is provided. The ethnic populationsare defined by the HapMap Project, where CEU represents individuals ofNorthern and Western Europe descent, HCB represents Han Chinese inBeijing, JAP represents Japanese in Tokyo, and YR1 represents the Yorubain Ibadan, Nigeria.

TABLE 2 MAF MAF MAF MAF SNP CEU HCB JAP YRI rs11166512 0.43 0.41 0.500.49 rs11184494 0.50 0.40 0.48 0.50 rs11247894 0.43 0.39 0.32 0.44rs12089156 0.46 0.49 0.44 0.43 rs12125888 0.40 0.43 0.48 0.43 rs121363700.42 0.48 0.42 0.48 rs12143315 0.40 0.42 0.42 0.42 rs12759642 0.39 0.480.48 0.42 rs156988 0.46 0.40 0.45 0.41 rs2050927 0.44 0.50 0.41 0.49rs213624 0.48 0.44 0.40 0.34 rs2454175 0.46 0.48 0.43 0.40 rs43295200.45 0.43 0.40 0.44 rs4487973 0.47 0.43 0.44 0.40 rs454782 0.48 0.400.41 0.46 rs4648888 0.33 0.30 0.33 0.46 rs635364 0.49 0.40 0.46 0.43rs660279 0.41 0.49 0.50 0.39 rs6687785 0.48 0.46 0.48 0.44 rs75511880.46 0.49 0.45 0.46 rs9431593 0.41 0.43 0.49 0.40

A multiplexed panel of 16 SNPs was analyzed with maf>0.3 in the samematernal plasma DNA extraction and established a baseline of maternalgenotypes by analyzing DNA from PBMCs. Using the maternal genotypeinformation, paternally-inherited alleles were identified in plasmasamples and estimated the amount of fetal DNA from the peak area ratioof extension products representing paternally-inherited fetal allelesand maternal alleles.

The AMG XY frequency was then compared with the allele-frequency ofpaternally-inherited fetal alleles in informative SNPs. This comparisonrevealed that samples with a positive Y-frequency of 10% (used as aLimit-of-quantitation threshold) or more have significantly higherdifferences between maternally and paternally-inherited fetalallele-frequencies (p-value <0.001; Fishers' exact test). This datashows that Fetal Identifiers can be used as a non-gender specificapproach for identification of the presence of fetal DNA. FIG. 8exemplifies those results.

Example 3 Multiplex Schemes

The above described RhD, fetal identifier and sex test may be runsimultaneously in various multiplex schemes. Exemplary multiplex schemesare provided in FIG. 10. For example, in the Scenario 1 assay, twomultiplex reactions are run in parallel. In the MP1, the followingreactions are performed: 10 Fetal Identifiers reactions, the RhD 4reaction, the RhD 10 reaction and the SRY reaction. In the MP2, thefollowing reactions are performed: 11 Fetal Identifiers reactions, theRhD 4 psi quantitative reaction, the RhD 5 reaction and the RhD 7reaction. Other exemplary multiplex schemes are provided in FIG. 10, butare not intended to limit the scope of the invention.

The PCR primers and extend primers for MP1 and MP2 are provided below inTable 3. Lower case nucleotides in the extend primer sequence representnon-template nucleotides that are added as mass modifiers. Additionalfetal identifiers which may be used as described herein are provided inTable 4.

TABLE 3 Multiplex Primer Name Amplification primer Amplification primerExtend Primer sequence MP1 RhD-10-3r-i ACGTTGGATGACGCTCATGAACGTTGGATGAACTCCATTT gGTCTCCAATGTTCGCGCAGGCAC CAGCAAAGTC TCTCTGACTC(SEQ ID NO: 15) (SEQ ID NO: 12) (SEQ ID NO: 13) MP1 RhD-4-3r-iACGTTGGATGCTGCCAAAGC ACGTTGGATGTGGCAGACAA GAACGGAGGATAAAGATCAGACTCTACACG ACTGGGTGTC (SEQ ID NO: 17) (SEQ ID NO: 1) (SEQ ID NO: 2) MP1rs7551188 ACGTTGGATGATCCCTGGTT ACGTTGGATGGAGCCTCTCA GGACAGATTCTGGGACCCTTCCTTAG GTGTCTATAC (SEQ ID NO: 29) (SEQ ID NO: 27) (SEQ ID NO: 28)MP1 rs11247894 ACGTTGGATGATCCTAGATA ACGTTGGATGGGAGGAAAGACCAAAGCCAAGAATTCA GCCCAAAGCC GAAGATTGTG (SEQ ID NO: 32) (SEQ ID NO: 30)(SEQ ID NO: 31) MP1 rs6687785 ACGTTGGATGATGCTGTAAA ACGTTGGATGTTCTCCTCTGCCTCAACAGTACACTTAATC GAGCCTCAAC ACCTGCTTTC (SEQ ID NO: 35)(SEQ ID NO: 33) (SEQ ID NO: 34) MP1 rs4487973 ACGTTGGATGTCAGAGAGTGACGTTGGATGGAATGCATGC cAGGTCACACAGTTAGGATT ACAAGACCTG CAACTTAGGG(SEQ ID NO: 38) (SEQ ID NO: 36) (SEQ ID NO: 37) MP1 rs4648888ACGTTGGATGCAGAGAGTCC ACGTTGGATGTGCCCAGACC aTGGACCTTCGGAAAGGATACCTGTTATTG AGAGAGGTCA (SEQ ID NO: 41) (SEQ ID NO: 39) (SEQ ID NO: 40)MP1 rs12089156 ACGTTGGATGGCTACATACT ACGTTGGATGCCTGCTGGCATACTATGTGGTCTCAACTATAT ATGTGGTCTC ACAAATCTTC (SEQ ID NO: 44)(SEQ ID NO: 42) (SEQ ID NO: 43) MP1 rs2050927 ACGTTGGATGTTCTAGCTTGACGTTGGATGTTGGGTGCAG TGCTTCTCCTCCATCATCCTTAGC CTTCTCCTCC AGTAGTCATC(SEQ ID NO: 47) (SEQ ID NO: 45) (SEQ ID NO: 46) MP1 rs12125888ACGTTGGATGCAACATCCTG ACGTTGGATGAGACAATTTC TACATGACTATCTCCTCCCTTAGGTTACATCACTC TGTCCTCTGG (SEQ ID NO: 50) (SEQ ID NO: 48) (SEQ ID NO: 49)MP1 rs12143315 ACGTTGGATGACAGGCATGA ACGTTGGATGTGCCATTGGTCCATCTTACCCAGCCTCTTTCTTCAA GCCATCTTAC ACAGTCACTC (SEQ ID NO: 53)(SEQ ID NO: 51) (SEQ ID NO: 52) MP1 rs213624 ACGTTGGATGTAGGTCAAGCACGTTGGATGTGTCCACCCA gGCCAAGGCCTCGGAGTCTGAACAGTT CAAGGCCTC GGAGCAGCCA(SEQ ID NO: 56) (SEQ ID NO: 54) (SEQ ID NO: 55) MP1 SRY_5-ibACGTTGGATGAGCATCTAGG ACGTTGGATGAGCAACGGGA cGTTACCCGATTGTCCTAC TAGGTCTTTGCCGCTACAG (SEQ ID NO: 57) (SEQ ID NO: 24) (SEQ ID NO: 25) MP2 RhD-4-psi-ACGTTGGATGGACTATCAGG ACGTTGGATGTGCGAACACG cTGCAGACAGACTACCACATGAAC 3r-iGCTTGCCCCG TAGATGTGAC (SEQ ID NO: 18) (SEQ ID NO: 5) (SEQ ID NO: 58) MP2RhD-5_3r-i ACGTTGGATGAATCGAAAGG ACGTTGGATGCTGAGATGGCATGCCGTGTTCAACACCTACTATGCT AAGAATGCCG TGTCACCACG (SEQ ID NO: 19)(SEQ ID NO: 7) (SEQ ID NO: 8) MP2 RhD-7-3r-i ACGTTGGATGAGCTCCATCAACGTTGGATGTTGCCGGCTC CTTGCTGGGTCTGCTTGGAGAGATCA TGGGCTACAA CGACGGTATC(SEQ ID NO: 22) (SEQ ID NO: 9) (SEQ ID NO: 10) MP2 rs660279ACGTTGGATGTTTCAGCAAC ACGTTGGATGTGCCCGTAAG CTTGATGTGCTTCCCTG CACTCTGAGCTAGGAGAGTG (SEQ ID NO: 61) (SEQ ID NO: 59) (SEQ ID NO: 60) MP2 rs635364ACGTTGGATGGAAATTTCTG ACGTTGGATGAGAGACTCCA TGGATTACTGGCAAAGAC GATTACTGGCTTTGTTTGGG (SEQ ID NO: 64) (SEQ ID NO: 62) (SEQ ID NO: 63) MP2 rs9431593ACGTTGGATGTTGAGATCAG ACGTTGGATGGCCTCAGTAG TGTTCCTGACTCTCAAAAT TGTCGGTTCCTCACATAAGG (SEQ ID NO: 67) (SEQ ID NO: 65) (SEQ ID NO: 66) MP2rs11166512 ACGTTGGATGCTTCATCCAC ACGTTGGATGTGACCAGATGCCACTATATCCACCTTTTCT TATATCCACC TTGGATTAG (SEQ ID NO: 70)(SEQ ID NO: 68) (SEQ ID NO: 69) MP2 rs4329520 ACGTTGGATGGAAAGTTGTCACGTTGGATGATGTCCACCT GCGTGGTTCTAGACTTATGC GTGGTAGAGG CCTGCTCCAC(SEQ ID NO: 73) (SEQ ID NO: 71) (SEQ ID NO: 72) MP2 rs454782ACGTTGGATGCTGTTAAGAT ACGTTGGATGCTGTCTTCCT AACTCCCATATTAGTCCACAGGCCAACTCCC CATTGCTCTG (SEQ ID NO: 76) (SEQ ID NO: 74) (SEQ ID NO: 75)MP2 rs12136370 ACGTTGGATGGAGTAGTTCT ACGTTGGATGCTCCTGGAAAgGCAGTAAGCTATTCTTGGGG TTGCAGTAAGC ACAGCAAAAG (SEQ ID NO: 79)(SEQ ID NO: 77) (SEQ ID NO: 78) MP2 rs12759642 ACGTTGGATGATTCTTCCTGACGTTGGATGGGAAATACCA caTCGGGATTCCCTGAACAAAA GGACTCAGAC GCAACCACAG(SEQ ID NO: 82) (SEQ ID NO: 80) (SEQ ID NO: 81) MP2 rs11184494ACGTTGGATGAGCTGGCCAT ACGTTGGATGGCCAATCTAT ATTTGACTTTCCTACTCCTTAACGTTTATTTGAC GAAGAATTAC (SEQ ID NO: 85) (SEQ ID NO: 83) (SEQ ID NO: 84)MP2 rs2454175 ACGTTGGATGGGAATCAGAC ACGTTGGATGGCCCAGCAGGcCTTCAAGGATTGGAATTAGAGT CTGTAAACAC ACACTTTTAT (SEQ ID NO: 88)(SEQ ID NO: 86) (SEQ ID NO: 87) MP2 rs156988 ACGTTGGATGAAAGCTCTGTACGTTGGATGGAAAGGGCTA tCGTCTCGGTCCTTCCTTTTCACTT GATGCGTCTC TGTAAGGAGG(SEQ ID NO: 91) (SEQ ID NO: 89) (SEQ ID NO: 90)

TABLE 4 Multiplex SNP_ID Amplification primer Amplification primerExtend Primer sequence W1 rs10793675 ACGTTGGATGAAGAGATGAGACGTTGGATGCTCTGTATTT AACGGCTCAACAGTT ACAGACTGGG ATAGCTTTC(SEQ ID NO: 94) (SEQ ID NO: 92) (SEQ ID NO: 93) W1 rs1829309ACGTTGGATGATCTCTGAGT ACGTTGGATGTTCCTAATCA TTGCTTTGGGGAGCAG TGACACCACCGGAGAGACCG (SEQ ID NO: 97) (SEQ ID NO: 95) (SEQ ID NO: 96) W1 rs6602279ACGTTGGATGTTTCAGCAAC ACGTTGGATGTGCCCGTAAG CTTGATGTGCTTCCCTG CACTCTGAGCTAGGAGAGTG (SEQ ID NO: 61) (SEQ ID NO: 59) (SEQ ID NO: 60) W1 rs635364ACGTTGGATGGAAATTTCTG ACGTTGGATGAGAGACTCCA TGGATTACTGGCAAAGAC GATTACTGGCTTTGTTTGGG (SEQ ID NO: 64) (SEQ ID NO: 62) (SEQ ID NO: 63) W1 rs9431593ACGTTGGATGTTGAGATCAG ACGTTGGATGGCCTCAGTAG TGTTCCTGACTCTCAAAAT TGTCGGTTCCTCACATAAGG (SEQ ID NO: 67) (SEQ ID NO: 65) (SEQ ID NO: 66) W1 rs11166512ACGTTGGATGCTTCATCCAC ACGTTGGATGTGACCAGATG CCACTATATCCACCTTTTCTTATATCCACC TTTGGATTAG (SEQ ID NO: 70) (SEQ ID NO: 68) (SEQ ID NO: 69) W1rs4329520 ACGTTGGATGGAAAGTTGTC ACGTTGGATGATGTCCACCT GCGTGGTTCTAGACTTATGCGTGGTAGAGG CCTGCTCCAC (SEQ ID NO: 73) (SEQ ID NO: 71) (SEQ ID NO: 72) W1rs454782 ACGTTGGATGCTGTTAAGAT ACGTTGGATGCTGTCTTCCT AACTCCCATATTAGTCCACAGGCCAACTCCC CATTGCTCTG (SEQ ID NO: 76) (SEQ ID NO: 74) (SEQ ID NO: 75) W1rs12136370 ACGTTGGATGGAGTAGTTCT ACGTTGGATGCTCCTGGAAAgGCAGTAAGCTATTCTTGGGG TTGCAGTAAGC ACAGCAAAAG (SEQ ID NO: 79)(SEQ ID NO: 77) (SEQ ID NO: 76) W1 rs12759642 ACGTTGGATGATTCTTCCTGACGTTGGATGGGAAATACCA caTCGGGATTCCCTGAACAAAA GGACTCAGAC GCAACCACAG(SEQ ID NO: 82) (SEQ ID NO: 80) (SEQ ID NO: 81) W1 rs11184494ACGTTGGATGAGCTGGCCAT ACGTTGGATGGCCAATCTAT ATTTGACTTTCCTACTCCTTAACGTTTATTTGAC GAAGAATTAC (SEQ ID NO: 85) (SEQ ID NO: 83) (SEQ ID NO: 84)W1 rs2454175 ACGTTGGATGGGAATCAGAC ACGTTGGATGGCCCAGCAGGcCTTCAAGGATTGGAATTAGAGT CTGTAAACAC ACACTTTTAT (SEQ ID NO: 88)(SEQ ID NO: 86) (SEQ ID NO: 87) W1 rs1452628 ACGTTGGATGGCTTGTGCTTACGTTGGATGGGTCAAGCAA acatAGTTATTCCTAGGGCTTCTC TGTTGTGTGG AGGCTTCAAG(SEQ ID NO: 100) (SEQ ID NO: 98) (SEQ ID NO: 99) W1 rs156988ACGTTGGATGAAAGCTCTGT ACGTTGGATGGAAAGGGCTA tCGTCTCGGTCCTTCCTTTTCACTTGATGCGTCTC TGTAAGGAGG (SEQ ID NO: 91) (SEQ ID NO: 89) (SEQ ID NO: 90) W1rs4570430 ACGTTGGATGACCCGAGCCA ACGTTGGATGGCACATGGAGGGTATCATAAGATACCTATGATGTC ATCAGGTATC ATGAATGGTC (SEQ ID NO: 103)(SEQ ID NO: 101) (SEQ ID NO: 102) W1 rs12062414 ACGTTGGATGTGCGTCAACCACGTTGGATGGGAAAGTCCT ggaaTTTCCAGTTCTATTCCAGCCTC TTTCCAGTTC CGACTGTTTG(SEQ ID NO: 106) (SEQ ID NO: 104) (SEQ ID NO: 105) W1 rs7545381ACGTTGGATGCCAGTCAAGC ACGTTGGATGGTGAGCACAA tccCTGAATGACAAAAGGGGAAGATATAAGGACAAA CTGTGTTCTA (SEQ ID NO: 109) (SEQ ID NO: 107) (SEQ ID NO: 108)W1 rs6427673 ACGTTGGATGGGACTAAAAC ACGTTGGATGGTCTCTCTAGccctcGCCAAACTTAGACCAAGGACAAC AGGGCCAAAC TACTAGTAAC (SEQ ID NO: 112)(SEQ ID NO: 110) (SEQ ID NO: 111) W1 rs10802761 ACGTTGGATGTCTTCTAAAAACGTTGGATGGGATGAGGTT AGTTATGAAATAAGTTTTATTCATTTAC TGTAGTTATG TTGACTAAGC(SEQ ID NO: 115) (SEQ ID NO: 113) (SEQ ID NO: 114) W2 rs642449ACGTTGGATGCCAAAAAACC ACGTTGGATGAGATTGCCTC CCTCTGCCTCCCCTA ATGCCCTCTGTCCATGTGAC (SEQ ID NO: 118) (SEQ ID NO: 116) (SEQ ID NO: 117) W2rs4839419 ACGTTGGATGCTGCCGCATC ACGTTGGATGATGTGTTTGT CCTTCACAAAGCCGACCTTCACAA GGCCACTTCC (SEQ ID NO: 121) (SEQ ID NO: 119) (SEQ ID NO: 120)W2 rs9324198 ACGTTGGATGAAAGGCCTAC ACGTTGGATGCAAAATATGT cGTTTGCTGGAAGCCTTGTTTGCTGG GTGAATCAGC (SEQ ID NO: 124) (SEQ ID NO: 122) (SEQ ID NO: 123)W2 rs1192619 ACGTTGGATGGCTCAACTCT ACGTTGGATGCCAGGAATGG TGGCCAGAAGAAGGAGGAACCAATCG GCATGTGTTC (SEQ ID NO: 127) (SEQ ID NO: 125) (SEQ ID NO: 126)W2 rs4657868 ACGTTGGATGCTAACCAGGA ACGTTGGATGCTAGCGTACCAGACACCCCCATACATTA AAAGACACCC CAATGGAATC (SEQ ID NO: 130)(SEQ ID NO: 128) (SEQ ID NO: 129) W2 rs6426873 ACGTTGGATGTAAATCAGGGACGTTGGATGAAGTGCTAGG cccCTGCCTTCTCTTCCAA CTGCCTTCTC GTTACAGGTG(SEQ ID NO: 133) (SEQ ID NO: 131) (SEQ ID NO: 132) W2 rs438981ACGTTGGATGTGTGCAAATT ACGTTGGATGGAACATTGGT ATGGACCACAAAAAACTTA GGCTAACATATTTAAACTC (SEQ ID NO: 136) (SEQ ID NO: 134) (SEQ ID NO: 135) W2rs12125888 ACGTTGGATGAGACAATTTC ACGTTGGATGCAACATCCTGTCTGTCCTCTGGTATCCTCT TGTCCTCTGG TACATCACTC (SEQ ID NO: 137)(SEQ ID NO: 49) (SEQ ID NO: 48) W2 rs3128688 ACGTTGGATGATCAAGAGGAACGTTGGATGGATTTACTCA cAAAATGGACAGAAGTTGAA AAATGGACAG ACTCTCTGGG(SEQ ID NO: 140) (SEQ ID NO: 138) (SEQ ID NO: 139) W2 rs4987351ACGTTGGATGGTGCATGGGC ACGTTGGATGCCAAACAGGG gCATCTAGACACATTTTGTGCTCATCTAGAC CCAATGGTAG (SEQ ID NO: 143) (SEQ ID NO: 141) (SEQ ID NO: 142)W2 rs6692911 ACGTTGGATGCTATTCCCTC ACGTTGGATGATTAAGATGGtccAAGAGCATTTTTCCTCTTC CTCAAAGAGC GTAGTTAAG (SEQ ID NO: 146)(SEQ ID NO: 144) (SEQ ID NO: 145) W2 rs6684679 ACGTTGGATGTATGTTACTTACGTTGGATGTCTTAAGGTG ggaCCACTGAGGAGATACACTA GCCTTGGCCC TCTCCCTCTG(SEQ ID NO: 149) (SEQ ID NO: 147) (SEQ ID NO: 148) W2 rs4320829ACGTTGGATGGGTTCTATGG ACGTTGGATGTGCTAGACAC ggtcACCTCTTTTCATAACAGGACTTTGGTGAG TTTAACTGCC (SEQ ID NO: 152) (SEQ ID NO: 150) (SEQ ID NO: 151)W2 rs4658481 ACGTTGGATGCTGCTAAGCA ACGTTGGATGGTGGTAGAAAatacGCATGAGAGAAAGGGAAAG TGAGAGAAAG CAAATGTCAGC (SEQ ID NO: 155)(SEQ ID NO: 153) (SEQ ID NO: 154) W2 rs3768458 ACGTTGGATGCCAAATGTCTACGTTGGATGGAGTTTATGT CTTAGTTACAAAGAAAATTGTGAG TAGTTACAAAG AATGTCAAC(SEQ ID NO: 158) (SEQ ID NO: 156) (SEQ ID NO: 157) W2 rs860954ACGTTGGATGTAGCCTTTAG ACGTTGGATGCCATTCTTGT TCTTGATGCCTTACAAAATAAATATTCTTGATGCC ATGTTTTGTC (SEQ ID NO: 161) (SEQ ID NO: 159) (SEQ ID NO: 160)W2 rs10453878 ACGTTGGATGGAGGAGCTAA ACGTTGGATGGGGATATGAAAAACAAATCCTCCTTTCTTTTAATTC CAAGTAGGAC TTACAACAGAG (SEQ ID NO: 164)(SEQ ID NO: 162) (SEQ ID NO: 163) W2 rs10753912 ACGTTGGATGGAGATTATATACGTTGGATGATTCTTCTAA GAGATTATATGTCTCTTTAATATTGTC GTCTCTTTAA CTTTTAGGC(SEQ ID NO: 167) (SEQ ID NO: 165) (SEQ ID NO: 166) W2 rs1637944ACGTTGGATGCTAATGCCTC ACGTTGGATGAATAGCAAAC cccccATATCATTTGCAATTGCATGGTTCTTTTCTTCC AACAGGTGGG (SEQ ID NO: 170) (SEQ ID NO: 168) (SEQ ID NO: 169)W2 rs4839282 ACGTTGGATGGAATCCTGGC ACGTTGGATGTGGGTTCACAgatgTCTCTTAAAGAGCAAAAAGCTAAG AGCTCATTAG TGAGTCTTGC (SEQ ID NO: 173)(SEQ ID NO: 171) (SEQ ID NO: 172)

Multiplex scheme 3 in FIG. 10 includes an albumin assay which may beperformed to determine total copy number of DNA molecules for the humanserum albumin gene. The albumin assay is useful to measure how much DNAis loaded into a particular reaction. It acts as an internal control anda guide to the likelihood of success for a particular PCR reaction. Forexample, if only 400 copies of ALB are measured then the probability ofdetecting any fetal DNA is very low. Primers for the Albumin assay areprovided in FIG. 4.

The entirety of each patent, patent application, publication anddocument referenced herein hereby is incorporated by reference. Citationof the above patents, patent applications, publications and documents isnot an admission that any of the foregoing is pertinent prior art, nordoes it constitute any admission as to the contents or date of thesepublications or documents.

Modifications may be made to the foregoing without departing from thebasic aspects of the invention. Although the invention has beendescribed in substantial detail with reference to one or more specificembodiments, those of ordinary skill in the art will recognize thatchanges may be made to the embodiments specifically disclosed in thisapplication, yet these modifications and improvements are within thescope and spirit of the invention.

The invention illustratively described herein suitably may be practicedin the absence of any element(s) not specifically disclosed herein.Thus, for example, in each instance herein any of the terms“comprising,” “consisting essentially of,” and “consisting of” may bereplaced with either of the other two terms. The terms and expressionswhich have been employed are used as terms of description and not oflimitation, and use of such terms and expressions do not exclude anyequivalents of the features shown and described or portions thereof, andvarious modifications are possible within the scope of the inventionclaimed. The term “a” or “an” can refer to one of or a plurality of theelements it modifies (e.g., “a reagent” can mean one or more reagents)unless it is contextually clear either one of the elements or more thanone of the elements is described. The term “about” as used herein refersto a value within 10% of the underlying parameter (i.e., plus or minus10%), and use of the term “about” at the beginning of a string of valuesmodifies each of the values (i.e., “about 1, 2 and 3” is about 1, about2 and about 3). For example, a weight of “about 100 grams” can includeweights between 90 grams and 110 grams. Thus, it should be understoodthat although the present invention has been specifically disclosed byrepresentative embodiments and optional features, modification andvariation of the concepts herein disclosed may be resorted to by thoseskilled in the art, and such modifications and variations are consideredwithin the scope of this invention.

Embodiments of the invention are set forth in the claims that follow.

1. A method for quantifying the fraction of a nucleic acid allele in a sample, comprising: (a) amplifying one or more regions containing a polymorphic site in sample nucleic acid, thereby generating amplified nucleic acid, wherein the sample nucleic acid contains nucleic acid from different sources; (b) sequencing the amplified nucleic acid, thereby providing nucleotide sequences; (c) quantifying a first allele and a second allele of the polymorphic site from the nucleotide sequences, wherein the first allele is from a first source and the second allele is from a second source; and (d) determining the fraction of the first allele or the second allele in the sample nucleic acid from the quantification in (c).
 2. The method of claim 1, wherein the fraction of the first allele is representative of the fraction of the sample nucleic acid from the first source.
 3. The method of claim 1, wherein determining the fraction of the first allele in the sample nucleic acid in step (d) is by comparing the quantity of the first allele to the sum of the quantity of the first allele and the quantity of the second allele.
 4. The method of claim 1, wherein determining the fraction of the second allele in the sample nucleic acid in step (d) is by comparing the quantity of the second allele to the sum of the quantity of the first allele and the quantity of the second allele.
 5. The method of claim 1, wherein one or more polymorphic regions comprise a single nucleotide polymorphism.
 6. The method of claim 1, wherein more than one region is amplified in (a).
 7. The method of claim 6, wherein at least 10 regions are amplified in (a).
 8. The method of claim 1, wherein the different sources are fetal and maternal.
 9. The method of claim 1, wherein the sample nucleic acid is from blood.
 10. The method of claim 1, wherein the sample nucleic acid is from plasma.
 11. The method of claim 1, wherein the sample nucleic acid is from serum.
 12. The method of claim 1, wherein the sample nucleic acid is extracellular nucleic acid. 